Chromosomal-level genome of macadamia(Macadamia integrifolia)

Macadamia from the family Proteaceae is a plant native to Australia and has long been favoured by people for its crispy and high nutritional and medicinal value.Here,the genome of GUIRE 1(GR1),a highly heterozygous superior cultivar of macadamia nut,was sequenced and assembled using nanopore sequencing,and a 807-Mb genome(contig N50,1.9 Mb;scaffold N50,54.70 Mb)and 14 chromosomes were obtained.A total of 453 Mb(about 55.95%)repetitive sequences and 37,657 protein-coding genes were obtained by gene annotation and homologous protein comparison.Proteaceae diverged from Nelumbonaceae nearly 115.37 million years ago and from Rubiaceae about 140 million years ago.A genome-wide duplication(WGD)event occurred in macadamia 41 million years ago based on the WGD analysis.The functional enrichment analysis of M.integrifolia-specific gene families revealed their roles in signal transduction,protein phosphorylation,protein binding,and defense response.Here,a highly heterozygous genome of M.integrifolia was unlocked to provide a database for breeding and molecular mechanism research.

Tropical crops enter the era of genome editing

Besides staple crops such as rice and maize,other tropical crops grown primarily in the tropics,including cassava,sweet potato,sugarcane,papaya,pineapple,and banana,provide important materials for our daily lives and for agro-industrial purposes.The modern breeding of these crops however is hampered by their biological nature and genetic complexity.All of these tropical crops can be,and in some cases must be,propagated vegetatively for traditional cultivation.

Challenges and opportunities to improve tropical fruits in Hainan,China

Tropical fruits play a major role in the economic and social development of Hainan(China).Despite favorable climatic conditions,the yield of tropical fruits in Hainan remains low,in part due to the low genetic potential of currently grown tropical fruit varieties.Consequently,there is a need to improve yield potential by exploiting the genome and germplasm resources of tropical fruit species,minimizing post-harvest losses,and improving transportation standards.In this study,we intend to collect germplasm resources from a wide range of domestic and exotic sources to evaluate the genetic yield potential and nutritional quality of fruit using plant morphology,taxonomy and physiological parameters.In this review,we aim to identify current bottlenecks in the Hainan tropical fruit industry and propose solutions through the use of conventional breeding and new biotechnological tools,including the use of omics and CRISPR to enhance yield and tackle biotic and abiotic stresses of tropical fruit species.Producing new fruit cultivars in Hainan,either through conventional strategies or the use of genome editing technology such as CRISPR,could help improve the socioeconomic status of this region.Furthermore,increasing the genetic potential and production of new cultivars can help in meeting the demands of new trade agreements with various nations under the'One Belt,One Road'initiative,Boao Forum for Asia,ASEAN agreements,and the Shanghai Cooperation Organization.

Evolutionary genomics of structural variation in the tea plant,Camellia sinensis

Structural variants(SVs)are a type of genetic variation that contribute substantially to phenotypic diversity and evolution.Further study of SVs will help us understand the influence of SVs associated with tea quality and stress resistance and provide new insight into tea plant breeding improvement and genetic research.However,SVs have not been thoroughly discovered in the tea plant genomes.Herein,we constructed a large-scale SV map across a population of 107 resequenced genomes,including both ancient and cultivated tea plants.A total of 44,240 highconfident SVs were identified,including 34,124 DEL(deletions),4,448 DUP(duplications),2,503 INV(inversions),544 INS(insertions)and 2,621 TRA(translocations).In total,12,400 protein-coding genes were overlapped with SVs,of which 49.5%were expressed in all five tea tissues.SVbased analysis of phylogenetic relationships and population structure in tea plants showed a consistent evolutionary history with the SNP-based results.We also identified SVs subject to artificial selection and found that genes under domestication were enriched in metabolic pathways involving theanine and purine alkaloids,biosynthesis of monoterpenoid,phenylpropanoid,fatty acid,and isoflavonoid,contributing to traits of agronomic interest in tea plants.In addition,a total of 27 terpene synthase(TPS)family genes were selected during domestication.These results indicate that these SVs could provide extensive genomic information for tea quality improvement.

Nutritional value of domesticated duckweed variety DW2602 and its feeding effects on the growth performance and digestive activities of tilapia fingerlings

Duckweed are a family of fast-growing aquatic plants,in which wild plants of many species have been tested in animal feed.We domesticated a duckweed variety,Spirodela polyrhiza DW2602,which had 44.5%protein and 2.6% lysine and was grown on a large scale.The effects of DW2602 on the growth performance and the digestive enzyme activities of tilapia variety GIFT(Genetic Improvement of Farmed Tilapia,Oreochromis niloticus)fingerlings were evaluated.The dry powder of DW2602 was added to conventional tilapia feed at six inclusion levels of 0%,10%,15%,20%,25%,and 30%.The diets were fed to tilapia fingerlings with an initial weight of 2.0±0.15 g for 60 d.Results showed that DW2602 improved the growth performance and digestive enzyme activities significantly.The feeding effect was the best when the inclusion rate was 20%,in which the body weight increased to 37.24±1.21 g in 60 d,18.15%higher than the control(P<0.05).The weight gain rate,the specific growth rate,the condition factor,and the hepatosomatic index of the fish were all significantly higher than the control(P<0.05),and the amylase,protease,and lipase activities in the digestive system were all promoted by DW2602(P<0.05).Therefore,the duckweed variety DW2602 has great application prospect in tilapia culture.

Inaugural Editorial

Tropical plants in the world include 2/3 of higher plant species,covering a large number of cash crops and their wild relatives.They have extremely rich genetic diversities and provide humans with food and beverages,energy,medicine,wood,fuel,various industrial raw materials,etc..They also provide necessary oxygen,water,living environment for other animals and plants,having irreplaceable functions on the health of the ecosystem.Due to the fragility of tropical forest ecosystems caused by human activities,it is necessary and urgent to protect the rare and endangered tropical plants and their habitats.

Research progress on the MYB transcription factors in tropical fruit

Tropical fruits,such as bananas,passion fruit,mangoes,and lychees,are rich in vitamins,flavonoids and non-flavonoid phenols,and are the healthiest way to intake bioactive compounds in one's daily diet.Coupled with their unique taste,tropical fruits are becoming more increasingly popular.The production of bananas is second only after grapes,while other tropical fruit are limited by the planting environment,resulting in a relatively low planting area and yield.With the improvement in breeding technology and planting technology,the development of tropical fruit crops will have broad prospects.MYB plays a major regulatory role in several biological processes,including growth and development of plants,quality formation,and stress resistance.There is a comparatively junior level of research on tropical fruit crops compared to grain fruit and model plants.Despite the progress that has been made in the development of molecular biology methods that can transform the genetic makeup of tropical fruit crops,the functional understanding of the multiple MYB genes is still in its initial stages.This paper aims to review the current status of the research on the development of these genes and their prospects.It is expected to provide a reference for the study of MYB transcription factors in tropical fruit crops and to provide new ideas for the functional resolution of MYB transcription factors in different biological processes.

De novo assembly of plant complete genomes

Plant genomes encode the mysteries of how plants cope with complex environments over long evolutionary histories.Over the past 20 years,rapidly developing technologies have allowed the decoding of hundreds of plant draft or reference genomes.The diversity,polyploidy and heterozygosity of plants make it technically challenging and time-consuming to generate high-quality plant genome assemblies.Recently invented ultra-long read sequencing technologies have achieved a milestone where several plant genomes have been gapless and assembled into telomere to telomere.Telomere-to-telomere(T2T)genome refers to a high-quality complete genome with high genomic accuracy,high continuity,and high integrity.With the release of the completed human genome and Arabidopsis thaliana genome,the era of complete T2T species genome has arrived.In this review,we summarize the history leading up to the gap free plant genomes based on emerging ultra-long read sequencing technologies.We discuss to close gaps relying on targeted genome sequencing and assembling technologies.However,there are still quite a lot of challenges in super large,polyploidy,and unstable genomes.Nevertheless,these complete genomes have already provided unprecedented information,which will certainly deepen our understanding of plant genomes and the exploration of more functional sequences.By taking advantage of the complete genomes,a series of important genes could be annotated,which will help achieve the goal of genome design in crop species.

Cell signaling during drought and/or cold stress in cassava

Cassava(Manihot esculenta Crantz)is a root crop significant in food security and various bio-industrial applications such as animal feed,modified starch,and biofuels.Drought and cold stress are two major factors limiting cassava production qualitatively and quantitatively,for which plants have evolved mechanisms to overcome the impact of these two stressors.In recent years,significant progress has been achieved in understanding the response mechanism of cassava plants to stress signals to tolerate the above stresses.In this review,core stress-signaling pathways,including transcription factor(TF)-related regulatory networks,plant hormone signaling,reactive oxygen species(ROS)scavenging,and non-coding RNA(ncRNA)and alternative splicing(AS)that modify gene expression levels in response to drought and/or cold stress in cassava,are summarized.Understanding these stress signaling and responses will increase our ability to improve the crops tolerance to multiple stresses for agricultural sustainability and food security for the growing world population.

Identification and functional analysis of transcription factors related to coconut(Cocos nucifera L.)endosperm development based on ATAC-seq

Coconut(Cocos nucifera L.)is a member of the palm tree family(Arecaceae)and the only living species of the genus Cocos.In this paper,the regulatory relationship pathways between multiple transcription factors and functional genes were identified by combining ATAC-seq and RNAseq in coconut endosperm at four different developmental stages(fruit after pollination:7 months,8 months,9 months and 10 months,respectively).The results indicated that the peaks detected in the promoter-TSS area accounted for the largest proportion(11.99%)in the third stage.These results suggest that the chromatin open region of cells in this period is more functional and that there are more functional genes with active transcription.In addition,a large number of potential regulatory relationships between transcription factors and functional genes were detected via bioinformatics analysis at the genomic level.Among them,CnGATA20 was predicted to be an important transcription factor with a binding site on the promoter region of the CnOLE18 gene.The regulatory pathway by which CnGATA20 positively regulates the expression of CnOLE18 was further confirmed by yeast one-hybrid,protoplast transient expression and dual-luciferase reporter system experiments.The results provide a new research strategy for exploring the regulation at both the transcriptional and posttranscriptional levels during coconut endosperm growth and development.

Tyrosine promotes anthocyanin biosynthesis in pansy(Viola×wittrockiana)by inducing ABA synthesis

Viola×wittrockiana(pansy)is an important ornamental plant,particularly during winter and spring.In previous studies,we found that the tyrosine decarboxylase gene of pansy(VwTYDC)was expressed differently in blotched and non-blotched areas of pansy petals,suggesting that tyrosine may have a role in anthocyanin biosynthesis.In this study,we found that virus-induced gene silencing of VwTYDC caused an accumulation of pink pigmentation in pansy petals.Likewise,exogenous tyrosine treatment(TYRT)induced the formation of black stripes in nonblotched petal areas.Metabolome analysis indicated that the contents of two anthocyanins,cyanidin-3-O-glucoside and cyanidin-3-O-rutinoside,increased significantly in the TYRT areas.RT-qPCR results revealed that the anthocyanin-related genes VwHCT,VwC3′H,VwCHS,and VwUGT were upregulated in the same areas.Transcriptome analysis revealed that four genes involved in the abscisic acid(ABA)biosynthesis pathway(VwNCED,VwABA2,VwAAO3,and VwCYP707A)were significantly upregulated in the same TYRT areas.ABA content was measured by ESI-HPLCMS/MS,and ABA content was significantly higher in TYRT areas than in control areas.In addition,when exogenous ABA was spread onto nonblotched petal areas,anthocyanin biosynthesis genes were upregulated just as with tyrosine.Thus,transcriptome and metabolite analyses revealed a possible novel regulatory network for anthocyanin biosynthesis in which tyrosine induces ABA synthesis and ABA then promotes anthocyanin biosynthesis in pansy petals.

The receptor-like cytoplasmic kinase OsRLCK118 regulates plant development and basal immunity in rice(Oryza sativa L.)

Receptor-like cytoplasmic kinases(RLCKs),which belong to a large subgroup of receptor-like kinases in plants,play crucial roles in plant development and immunity.However,their functions and regulatory mechanisms in plants remain unclear.Here,we report functional characterization of OsRLCK118 from the OsRLCK34 subgroup in rice(Oryza sativa L.).Expression of OsRLCK118 could be induced by infections with Xanthomonas oryzae pv.oryzae(Xoo)strains PXO68 and PXO99.Silencing of OsRLCK118 altered plant height,flag-leaf angle and second-topleaf angle.Silencing of OsRLCK118 also resulted in increasing susceptibility to Xoo and Magnaporthe oryzae(M.oryzae)in rice plants.OsRLCK118 knock-out plants were more sensitive to bacterial blight whereas OsRLCK118 overexpressor plants exhibited increased disease resistance.Expression levels of pathogenesis-related genes of OsPAL1,OsNH1,OsICS1,OsPR1a,OsPR5 and OsPR10 were reduced in the rlck118 mutant compared to wild-type rice(Dongjin)and knock-out of OsRLCK118 compromised the production of reactive oxygen species.These results suggest that OsRLCK118 may modulate basal resistance to Xoo and M.oryzae,possibly through regulation of ROS burst and hormone mediated defense signaling pathway.

Banana somatic embryogenesis and biotechnological application

As one of the most important economic crops for both staple food and fruit widely cultivated in the tropics and subtropics,banana(Musa spp.)is susceptible to a plethora of abiotic and biotic stresses.Breeding cultivars resistant to abiotic and biotic stressors without adverse effects on yield and fruit quality are the objectives of banana improvement programs.However,conventional breeding approaches are time-consuming and severely hampered by inherent banana problems(polyploidy and sterility).Therefore,genetic transformation is becoming increasingly popular and can provide rapid solutions.Numerous efforts have been made to develop superior banana cultivars with better resistance to abiotic and biotic stresses and optimum yields using genetic modification strategies.Somatic embryogenesis(SE)through embryogenic cell suspension(ECS)cultures is an ideal recipient system for genetic transformation in banana.The purpose of this paper is to review the current status of banana somatic embryo research,clarify the process of banana somatic embryo induction and culture,and summarize the main influencing factors in the process of somatic embryogenesis.At the same time,their applications in breeding technologies such as cryopreservation,protoplast culture,genetic transformation and gene editing were also summarized,in order to provide reference for the research and practical application of banana somatic embryogenesis in the future.